$1,000 genome a mirage?

Years of talk about cutting the price of sequencing a human genome to $1,000 has made one prominent genomics guru more than a little cranky. Mick Watson wrote on his blog Tuesday that such talk is "utter crap."

Watson, a genomicist/bioinformatician who heads a genomics center at the Roslin Institute, isn't at all sheepish about voicing his disdain for popular and scientific media accounts of the impending $1,000 genome. What set him off was a marketing statement in the new journal PeerJ that talked of a $99 genome.

Two even more prominent genomics experts I contacted for comment, J. Craig Venter and Eric Topol, say Watson is both right and wrong. Right that the full cost of a human genome today is much more than $1,000. Wrong because the price of that genome continues to drop, so a $1,000 genome is indeed fast approaching.

But first, some details on Watson's complaint.

Watson says just the cost of chemicals for doing a medical-grade human genome runs to more than $1,000. (Because today's DNA sequencers are fast but far from error-free, genomes must be run many times -- at least 30x is the standard -- to eliminate errors. Venter and colleagues learned that the hard way when they synthesized a bacterial genome, put it in a host cell that had its DNA removed, and nothing happened. An apparently trivial mistake -- one base pair deleted -- made the whole genome fail. They tried again and succeeded, once they had fixed the error. That's the difference between research-grade and medical-grade genomes, Venter says.)

Throw in equipment depreciation, data storage, overhead, staff time and the need for genome sequencing companies to make money, Watson says, and the current cost is more than $2,000.

"Obviously, Illumina don’t charge themselves list price for reagents, and nor do LifeTech, so it’s possible that they themselves can sequence 30x human genomes and just pay whatever it costs to make the reagents and build the machines; but this is not reality and it’s not really how sequencing is done today," Watson wrote on his blog. "These guys want to sell machines and reagents, they don’t want to be sequencing facilities, plus they still have to pay the staff, pay the bills, make a profit and return money to investors."

"Sequencing cost is the only thing anyone measures and is approaching $1k in theory, the accuracy of whole genomes is not of diagnostic quality, and the informatics cost more than the sequencing," Venter said by email. "I have been saying this for years."

"Although many 'genome' companies and researchers are promoting personal genomics for medicine and/or life choices, regulation of data quality and standards is lacking, which has made deceptive marketing a reality in some instances," Venter wrote. "We have sequence and genetic data quality that is suitable for some scientific analyses but no standards adequate for clinical practice or even for informing individuals of results that exist. We have come a long way in genomics; however, for genome sequencing to reach its full potential we still have a long way to go."